The Mangalore and Udupi region on the south-west coast of India is characterized by small west-flowing rivers (150–250 km in length) originating in the Western Ghats (up to 1940 meters above sea level (m asl)) and joining the Arabian Sea. The area experiences a humid tropical climate with frequent, high-intensity rainfall (4000 mm annual average). Nevertheless, there is a shortage of water during the peak dry season immediately before the onset of monsoon because of a rapid fall in the groundwater level. From the humid high-altitude forests to the intense agriculture in the coastal area, there is an urgent need to understand the movement of water between evapotranspiration, rainfall, river systems and the groundwater compartments in order to achieve better water resource management. Demographic pressure on the area with over half a million inhabitants and industrial activity strongly influence this fragile ecosystem. The coastal area is characterized by shallow open wells, which are particularly sensitive to pollution and eutrophication. Stable water isotopes (18O and deuterium) were used for the first time in this region to determine the isotopic characteristics of the different waters. There is a clear seasonal difference in the isotopic ratios and d-excess values between the summer and winter monsoon periods, with a predominance of lighter isotopes in the latter period. No significant variations in isotopic ratios were observed in relation to altitude because of the possible role of mist formation at high altitude. Greater d-excess values were observed in the west-flowing streams than in rivers flowing east on account of the moist westerly oceanic winds and water vapour recycling. Copyright © 2011 John Wiley & Sons, Ltd.